Development of an oligonucleotide-based SNP detection method on lateral flow strips using hexapet tages

Detection of point mutations or single nucleotide polymorphisms (SNPs) is important in relation to disease susceptibility or detection in pathogens of mutations determining drug resistance or host range. There is an emergent need for rapid detection methods amenable to point-of-care applications. The purpose of this study was to reduce to practice a novel method for SNP detection and to demonstrate that this technology can be used downstream of nucleic acid amplification. The authors used a model system to develop an oligonucleotide-based SNP detection system on nitrocellulose lateral flow strips. To optimize the assay they used cloned sequences of the herpes simplex virus-1 (HSV-1) DNA polymerase gene into which they introduced a point mutation. The assay system uses chimeric polymerase chain reaction (PCR) primers that incorporate hexameric repeat tags ("hexapet tags"). The chimeric sequences allow capture of amplified products to predefined positions on a lateral flow strip. These "hexapet" sequences have minimal cross-reactivity and allow specific hybridization-based capture of the PCR products at room temperature onto lateral flow strips that have been striped with complementary hexapet tags. The allele-specific amplification was carried out with both mutant and wild-type primer sets present in the PCR mix ("competitive" format). The resulting PCR products carried a hexapet tag that corresponded with either a wild-type or mutant sequence. The lateral flow strips are dropped into the PCR reaction tube, and mutant sequence and wild-type sequences diffuse along the strip and are captured at the corresponding position on the strip. A red line indicative of a positive reaction is visible after 1 minute. Unlike other systems that require separate reactions and strips for each target sequence, this system allows multiplex PCR reactions and multiplex detection on a single strip or other suitable substrates. Unambiguous visual discrimination of a point mutation under room temperature hybridization conditions was achieved with this model system in 10 minutes after PCR. The authors have developed a capture-based hybridization method for the detection and discrimination of HSV-1 DNA polymerase genes that contain a single nucleotide change. It has been demonstrated that the hexapet oligonucleotides can be adapted for hybridization on the lateral flow strip platform for discrimination of SNPs. This is the first step in demonstrating SNP detection on lateral flow using the hexapet oligonucleotide capture system. It is anticipated that this novel system can be widely used in point-of-care settings.

Conventional detection methodology is limiting our ability to understand the roles and functions of fine roots

We lack a thorough conceptual and functional understanding of fine roots. Studies that have focused on estimating the quantity of fine roots provide evidence that they dominate overall plant root length. We need a standard procedure to quantify root length/biomass that takes proper account of fine roots. Here we investigated the extent to which root length/biomass may be underestimated using conventional methodology, and examined the technical reasons that could explain such underestimation. Our discussion is based on original X-ray-based measurements and on a literature review spanning more than six decades. We present evidence that root-length recovery depends strongly on the observation scale/spatial resolution at which measurements are carried out; and that observation scales/resolutions adequate for fine root detection have an adverse impact on the processing times required to obtain precise estimates. We conclude that fine roots are the major component of root systems of most (if not all) annual and perennial plants. Hence plant root systems could be much longer, and probably include more biomass, than is widely accepted.

An implementation of nonlinear multiuser detection in Rayleigh fading channel

A blind nonlinear interference cancellation receiver for code-division multiple-access- (CDMA-) based communication systems operating over Rayleigh flat-fading channels is proposed. The receiver which assumes knowledge of the signature waveforms of all the users is implemented in an asynchronous CDMA environment. Unlike the conventional MMSE receiver, the proposed blind ICA multiuser detector is shown to be robust without training sequences and with only knowledge of the signature waveforms. It has achieved nearly the same performance of the conventional training-based MMSE receiver. Several comparisons and experiments are performed based on examining BER performance in AWGN and Rayleigh fading in order to verify the validity of the proposed blind ICA multiuser detector.

Blind detection of PAM and QAM in fading channels

This correspondence considers block detection for blind wireless digital transmission. At high signal-to-noise ratio (SNR), block detection errors are primarily due to the received sequence having multiple possible decoded sequences with the same likelihood. We derive analytic expressions for the probability of detection ambiguity written in terms of a Dedekind zeta function, in the zero noise case with large constellations. Expressions are also provided for finite constellations, which can be evaluated efficiently, independent of the block length. Simulations demonstrate that the analytically derived error floors exist at high SNR.

Population-based detection of systolic and diastolic dysfunction with amino-terminal pro-B-type natriuretic peptide

Background There is limited information regarding the clinical utility of amino-terminal pro-B-type natriuretic pepticle (NT-proBNP) for the detection of left ventricular (LV) dysfunction in the community. We evaluated predictors of circulating NT-proBNP levels and determined the utility of NT-proBNP to detect systolic and diastolic LV dysfunction in older adults. Methods. A population-based sample of 1229 older adults (mean age 69.4 years, 50.1% women) underwent echocardiographic assessment of cardiac structure and function and measurement of circulating NT-proBNP levels. Results Predictors of NT-proBNP included age, female sex, body mass index, and cardiorenal parameters (diastolic dysfunction [DID] severity; LV mass and left atrial volume; right ventricular overload; decreasing ejection fraction [EF] and creatinine clearance). The performance of NT-proBNP to detect any degree of LV dysfunction, including mild DID, was poor (area under the curve 0.56-0.66). In contrast, the performance of NT-proBNP for the detection of EF 0.90 regardless of age and sex; history of hypertension, diabetes, coronary artery disease; or body mass category. The ability of NT-proBNP to detect EF

Implementing ICA in blind multiuser detection

This paper introduces a blind multiuser detection algorithm for MIMO channels. The receiver is required to separate and recover the information signal of the desired user(s) based on independent component analysis (ICA) of the received sequence. The received sequence is assumed to be independent identically distributed. Experimental results show that the proposed blind ICA multiuser detection works well with a short symbol sequence, even if the channel time span is not accurately estimated. It is concluded that the proposed blind multiuser detection performs better than the conventional matched filters in a noisy environment.

Methods for conflict resolution in policy-based management systems

While developments in distributed object computing environments, such as the Common Object Request Broker Architecture (CORBA) [17] and the Telecommunication Intelligent Network Architecture (TINA) [16], have enabled interoperability between domains in large open distributed systems, managing the resources within such systems has become an increasingly complex task. This challenge has been considered for several years within the distributed systems management research community and policy-based management has recently emerged as a promising solution. Large evolving enterprises present a significant challenge for policy-based management partly due to the requirement to support both mutual transparency and individual autonomy between domains [2], but also because the fluidity and complexity of interactions occurring within such environments requires an ability to cope with the coexistence of multiple, potentially inconsistent policies. This paper discusses the need of providing both dynamic (run-time) and static (compile-time) conflict detection and resolution for policies in such systems and builds on our earlier conflict detection work [7, 8] to introduce the methods for conflict resolution in large open distributed systems.

Noise in detection of qubit states using a quantum point contact

We present a model for detection of the states of a coupled quantum dots (qubit) by a quantum point contact. Most proposals for measurements of states of quantum systems are idealized. However in a real laboratory the measurements cannot be perfect due to practical devices and circuits. The models using ideal devices are not sufficient for describing the detection information of the states of the quantum systems. Our model therefore includes the extension to a non-ideal measurement device case using an equivalent circuit. We derive a quantum trajectory that describes the stochastic evolution of the state of the system of the qubit and the measuring device. We calculate the noise power spectrum of tunnelling events in an ideal and a non-ideal quantum point contact measurement respectively. We found that, for the strong coupling case it is difficult to obtain information of the quantum processes in the qubit by measurements using a non-ideal quantum point contact. The noise spectra can also be used to estimate the limits of applicability of the ideal model.